The Puppetmaster
by dumbledoresarmyat221b
Summary: Sherlock is back in the game, but so is James Moriarty. And this time, Molly Hooper is his target. Sherlock will do anything to protect his friends, but will it be enough? A Sherlolly fanfic
1. Chapter 1

_Chapter 1_

 ** _Day 1: 1:13 pm: St. Bartholomew's Hospital_**

Sherlock paused just outside the door. Should he really be doing this? _Oh please,_ he thought to himself, _since when have you let the British government, or worse, Mycroft, stop you? Besides, she'll help me._

Sherlock opened the door just a crack to make sure his ears weren't deceiving him. Nope, they weren't, as they so rarely do. There was no one in the lab. He flung open the door to the lab at St. Bart's he had grown so fond of.

Sherlock was somewhat surprised; Molly was usually at work at this time. He was certain (and secretly hoping) that she would be there because he knew she would have the most satisfying response to his return. She would be so happy, not only to see that he was back, but also to know he was staying that she would let him do or use whatever he wanted. She had the first time.

A bit disappointed, Sherlock strode over to the microscope and took a dish out of one of his coat pockets. A few minutes later, Sherlock was completely lost in thought. A loud crash startled him, and he sat up and looked around. "Molly?" He asked hopefully. But he soon realized that the noise had come from out on the street and through the open window. He really needed to be more careful. _It's fine._ He thought. _Even if someone catches me in here and throws me out, I'll just endure the lecture from Mycroft and come straight back._

He could imagine Mycroft's pompous voice dripping with pleasure saying "I told you not to" when (or rather, IF) anyone caught him at the hospital. As per the terms of his release, he was not authorized to leave the flat without "permission". Sherlock unconsciously rolled his eyes. _Absolutely ridiculous_. He didn't need Mycroft spying on him wherever he went, and certainly not here. He was never actually "allowed" into the lab at Bart's. Technically, using their equipment was completely illegal. But he had been for years, so who's going to stop him now? He sighed. He knew someone would actually kick him out if they found him, so he had to be more cautious. He was aware that this was the best he was going to get, as his meeting with Mycroft from a few hours ago replayed in his head.

 ** _Day 1: 10:06 am: In transit to the Diogenes Club_**

"Hold still and follow the light." John held up a small flashlight to Sherlock's eyes and moved it slowly back and forth.

"I'm fine…" Sherlock rolled his eyes to John's chagrin.

"Just do it, Sherlock."

"Really, John. You act like I'm an amateur."

"Meaning you've overdosed before?" John brought down the flashlight and glared at him while he checked his pulse. Sherlock opened his mouth to retaliate, but decided against it.

Mary sat opposite them, puzzled in thought. "I still don't understand. I thought you said Moriarty shot himself in the head."

"Of course he did. I saw him." Sherlock stated bluntly, as if it were as plain as day.

"And you said you know what he's going to do next." Mary asked.

"Yes…. Your point being?"

"I think what she's trying to get at is how can he do anything if he's dead?" John pointed out. "Really, Sherlock, I think you should go to the hospital."

"Absolutely not. Besides, Mycroft is so paranoid he'll probably have a full medical staff waiting for me at his personal clubhouse." Sherlock hated that place, as he has verbalized to his brother a hundred times. Still, they keep requesting his membership. They never learn.

"Well, tell us then. What is he going to do and how's he going to do it? Enlighten us, I'm dying to know." Mary leaned back in her seat, smirking.

"There's no way he could be alive. He must've known that it would come to this, and set a plan in place in case he was forced into committing suicide. A plan to solve the final problem, once and for all."

"And the final problem would be…?" Mary asked. "Honestly, you two never fill me in on anything."

"I don't know yet, but I'm sure I'll learn soon enough." Sherlock said, with a considerable amount of frustration in his voice.

"That seems kind of unrealistic, Moriarty trusting someone else to carry out his most important plan." John pointed out. "You're absolutely sure he's dead? Absolutely sure? Maybe he's got a secret twin or something." He said with a chuckle.

"For the last time John, it's never twins! Now shut up, both of you. I need to think." Sherlock closed his eyes and sat back, completely immobile for the rest of the ride. Mary and John threw glances at each other, both trying not to laugh.

 ** _Day 1: 11:10 am: The Diogenes Club_**

"Mycroft, this is completely unnecessary." Sherlock fumed as a full arsenal of medical staff swarmed around him, trying to force IV drips and other such nonsense onto him.

"Well, since you've decided to be incomprehensibly under the influence at the most inopportune time, I need to do my best to snap you out of it. You need to be at the top of your game."

"I'm always at my best. I'm suddenly back in the game and couldn't be happier…. OW! Piss off!" Sherlock exclaimed as one of the nurses pricked his finger for a blood sample.

"Right, well, Lady Smallwood and I have come to an agreement on the terms of the suspension of your banishment."

"Terms?" Sherlock looked at his unceasingly annoying brother. "What terms? Just forget the whole Magnussen business, I did you all a favor."

"Mr. Holmes, that is not how the system works. You've broken the law, and even though we've decided to change your punishment because we believe you will be an asset in this situation, doesn't mean we can eliminate it entirely." Lady Smallwood shuffled with her papers and handed a few to Mycroft. "Now, we've decided to let you back into your flat and to continue with your detective work, however…. Mr. Holmes?"

Sherlock had completely ignored the woman in front of him and was…

"Give me that!" Mycroft exclaimed and practically wrestled his brother to the ground to get the phone out of his hands. Mycroft finally ripped the phone from Sherlock and glanced at the screen. "Are you tweeting?"

"Of course not. Twitter is a ridiculous concept invented by lonely people who have way too much time on their hands."

Mycroft glared at his brother over the phone. "That explains why you've just tweeted 'Alert the media: Sherlock Holmes is back in the game #Can'tKeepMeDown #FreeAsABird' "

"Mr. Holmes, please, let's get back to the debriefing. The sooner we finish, the sooner you can leave."

"Do we have to?" Sherlock grumbled.

"Sherlock, please. I know it's difficult for you, but try to cooperate." Mycroft said with as much sarcasm as he could muster.

"Now, Mr. Holmes, you've stated that you know where Moriarty is and what he's been up to?" Lady Smallwood put on her glasses and began scribbling on one of her papers.

"In a manner of speaking, yes." said Sherlock.

"You have been appointed as the head of this case, and will report to Mycroft with any news. Also, as I was going to say before, you will be allowed to continue to take individual cases, but you are not to leave the flat without permission."

"What?" exclaimed Sherlock, with exasperation in his voice. He did NOT need a babysitter.

"You will be under a sort of 'house arrest'. You will not leave the flat until you have informed Mycroft or myself of your destination and we have approved it. You are not to take any cases from the Scotland Yard. Detective Inspector Lestrade has volunteered to keep an eye on you and tell us if you've broken the terms of your release." Lady Smallwood explained as Sherlock stared in horror.

John and Mary, who had been quiet through the duration of the meeting, looked at each other and rolled their eyes.

"50 quid he breaks this in 24 hours," said Mary, smirking.

"No bet. I wouldn't even give him 6 hours." John said as Mary stifled a giggle.

Sherlock groaned. "So basically, I'm on parole while also saving England from a criminal mastermind?"

Lady Smallwood ignored him and continued. "And lastly, we have been informed that you, under no authority, have been utilizing St. Bartholomew's research hospital as a means for your own experiments. You are banned from the grounds."

"What? No!" Sherlock exclaimed rather loudly.

John and Mary looked at each other again, but this time with puzzled expressions. Why would he care, he has everything he needs in his makeshift kitchen lab anyway.

"They had every right to ban you from the facility in the first place, but this government order gave them the extra push. You've been banned, Sherlock. Understand?" Mycroft said haughtily.

"Hmph." Sherlock leaned back in his chair again and bit his lip. "Fine. Whatever. Are we finished? Can I leave?"

Mycroft rolled his eyes. As much of a necessity that Sherlock Holmes was, he was still a pain in the ass. "Yes, take Mr. and Mrs. Watson home, and then go to your flat. We'll be keeping an eye on you." He turned to Lady Smallwood. "Shall I escort you to your car?"

"Finally!" Sherlock leapt out of his seat, grabbed his coat and practically ran out the door.

 ** _Day 1: 1:18 pm: St. Bartholomew's Hospital_**

While from an outside eye it may have seemed like Sherlock was simply examining a blood sample under the microscope, he wasn't . He rarely did, contrary to popular belief. He was comfortable using the microscope, and so often used that as a cover when he needed to think without accessing his mind palace. People assumed he was working and would usually leave him alone. It was perfect.

Right. Onto the final problem. Moriarty was obviously going to try to target his friends again, especially now that the list has grown with Mary and the new baby. Breaking his one and only vow was not an option; he had to make them his priority. Which meant he had to find out what Moriarty's death wish was, and fast. More importantly, he needed to find out who Moriarty had trusted enough to carry out the rest of his plan. After finding them, and breaking them, compared to Moriarty himself, would be easy .

Sherlock took out his phone and texted a few members of his homeless network to station them around London so they could keep an eye out for any suspicious behavior. Then he started a message to John when…

"Sherlock!"

Sherlock looked up to see the petite Dr. Hooper standing in the doorway, carrying a small shopping bag, with her mouth hanging open.

"Wha… Um… How… Um… Hi!" Molly was at a loss for words. Again. Just Sherlock's presence seemed to do that to her. But what was he doing here?

"Hello, Molly. I was afraid you were out for the day. I might need your help."

"Oh, right. Well, I …"

"I assume you are aware of the dire situation at hand. You're quite peaky, your hands are shaking slightly, and the telly was left on. Since you were obviously quite taken aback by the broadcast of Moriarty, who has seemingly 'risen from the dead'" Sherlock rolled his eyes, "you should not be surprised that I'm here. My brother has insisted on the suspension of my banishment in return for my assistance in capturing Moriarty, or what's left of him at least. We've discussed a plan, and I'm going to need your help since I'm not technically allowed at Bart's anymore. Since you're here now, I could use…."

"Sherlock!" Molly stopped him midsentence, somewhat frustrated.

Surprised, Sherlock froze. "What?"

"I'm not staying. I left something in my locker and I just came back to get it."

"Oh. I see." He narrowed his eyes for a split second, then relaxed and turned back to his phone. "Because of your migraine. In case you weren't aware, acetaminophen is not usually as effective as naproxen or ibuprofen. If you have been having consistent migraines, I would recommend…"

"I don't!" She snapped. "PLEASE, just keep your opinions to yourself for once."

Sherlock sat bolt upright and stared.

"I'm sorry, that was rude. I don't normally get migraines, but I think seeing that video of Moriarty gave me a bit of a shock."

"Oh… I, um…. Yes, of course. If you are feeling under the weather you should rest." Sherlock was glad that Molly had finally started to stand up for herself, but he was still getting used to it. Curiously, the new outspoken Molly was much more tolerable than the meek and insecure Molly. Even somewhat attractive, if he let his guard down. _No,_ Sherlock thought to himself. _You need to focus on Moriarty._

"Thanks. I've never had one this bad before. The last migraine I had was in medical school, actually."

"However, I will require your assistance at some point, so please try to be prompt in replying to any of my messages. You are notoriously bad at that." Sherlock stated, oblivious to the fact that Molly had said anything to him.

"Right, of course." Molly sighed. She loved Sherlock, she really did. And not just in a romantic way, even though she still did after all these years. Why had she let herself fall for him again when he came back the first time? She almost never thought about him, and she had Tom (who turned out to be a lying cheat anyway). She knew he would never return the love she felt for him.

Not that he wasn't capable. She knew he was, even though he tried so hard to hide it. Either hide it from others or suppress it completely, she wasn't sure. Even if he trusted her and considered her his friend, he would never fall in love with her. Sometimes it seemed like he wanted to be more than friends, like that time when he first came back and took her out on a couple of cases with him. By Sherlock Holmes standards, he was definitely flirting with her, but then backed off when he noticed the ring. Or maybe she was just reading too much into it.

But she was still his friend. She enjoyed working with him, too. Just not today. She could barely think with the pounding headache and the growing nausea that came from the pit of her stomach.

"I'm just going to get the rest of my things. I guess I'll see you soon, Sherlock?"

"Yes." He said bluntly, without even looking up.

As always, short and to the point. Molly started walking towards the office.

"Molly? If you don't feel well enough to get home by yourself, I could escort you. If you'd like me to."

Molly stopped and turned. That was new. The only times he ever offered her something were when he had embarrassed her in front of all their friends at that Christmas party or when he offered her dinner the one day she assisted him on some cases. She wasn't going to let this opportunity slip away.

"Actually, that would be wonderful. I'm starting to feel a bit dizzy."

Sherlock nodded and stood up as Molly turned and started walking toward the office again, when she collapsed and started shaking uncontrollably.

"Molly!"

Sherlock ran to her side. He could practically see her heart beating out of her chest. _Don't panic,_ he thought to himself, _just call an ambulance. Wait, you idiot, we're in a hospital._ Sherlock rushed to move the chairs and other items out of range so she didn't accidently hurt herself, then ran as fast as he could to get help.


	2. Chapter 2

_**Hi everyone! Thanks for reading my first chapter! I'm really excited about the developing story!**_

 _**Sorry it has been taking me so long. I just want to make sure everything is perfect and I don't miss anything for later on :)**_

 _**Also, thank you all for your positive feedback! I really appreciate it!**_

 _**Just a hint for the next chapter - look up grayanotoxins if you want a spoiler - you might find something familiar :)**_

 _Chapter 2_

 ** _Day 1: 2:36 pm: University College Hospital_**

"Mild cardiac arrest, low blood pressure, extremely low oxygen levels. Currently unconscious but we expect that she will wake up soon. We're monitoring her vitals and everything seems to be returning to normal at a healthy rate." The doctor said as he shuffled through the file and then looked up at Sherlock and John. They were standing outside of the room Molly had been put in and had been waiting anxiously.

"Why did this happen? Have you found any underlying conditions that could have led to this?" John asked.

"Not yet. We're currently running some tests, and we're going to ask her some questions when she wakes up."

John was still in disbelief. "How could this have happened? She's healthy and young. Does she have a history of cardiac disease in her family?"

"No." Sherlock replied rather hastily. He hadn't said a word since the EMT's took Molly away, and John had noticed that he was fidgeting more than normal.

"Excuse me, Doctor? Miss Hooper needs your attention." The nurse gestured toward Molly's room. As the doctor retreated to see what the problem was, Sherlock dropped into the nearest chair and tapped his feet nervously.

"Sherlock, what happened when you were with her?"

"I told you already, John." The fidgeting didn't stop.

"Sherlock, the doctor said she would wake up soon. She'll be fine."

"Does this seem like a coincidence to you?" Sherlock said abruptly as he turned to face John.

"Does what seem like a coincidence?"

"That we get word of Moriarty's so-called return just before Molly is hospitalized? I think she was targeted. I knew this would happen!" Sherlock said loudly as he buried his face in his hands.

"Sherlock, I know you're worried…"

"I'm not worried."

John glared at him. "You know, being concerned for a friend isn't a bad thing."

Sherlock groaned. "I don't need that lecture right now, John."

"As I was saying, I think you're overreacting. We should wait until the tests come back. Geez, and you get mad when we say you're a drama queen."

"Hey, you two. How's she doing?" Greg Lestrade had just come up the stairs and was walking toward them.

"About time you showed up, Grant. Do you not consider Molly your friend? I texted you almost 30 minutes ago and you were at Scotland Yard when you received it. My contacts said that you didn't leave until 12 minutes ago. Don't even pretend like you care." Sherlock stated rather bluntly.

Lestrade opened his mouth to retaliate, but John interjected. "Ignore him, Greg. He's a little shaken."

"No I'm not!"

"Right…" Lestrade looked at Sherlock quizzically. "So?"

"She'll be all right." said John. "She had a mild heart attack, and it seems she passed out from hypoxemia."

"Oh God!" Lestrade took a deep breath and ran his hand through his hair.

"Relax, Greg, hypoxemia just means poor blood oxygenation." said John comfortingly.

"Here we go again with the doctor rubbish." Sherlock said as he fell further back in his chair and rubbed his temples.

John ignored him. "And having a mild heart attack is uncommon at her age, but not unheard of. She'll be back to herself in no time."

Lestrade continued to inquire about Molly's condition and interrogated Sherlock as to what had actually happened earlier. As they were talking, the nurse currently taking care of Molly left her room (rather hurriedly, Sherlock noticed) and came back a few minutes later with two new doctors. _Why would they be necessary?_ Sherlock thought to himself while following the doctors with his gaze.

John noticed the look of concern on Sherlock's face. "What is it?" He asked, as he turned towards the door.

"Two other doctors just went into her room. Why would she need them?"

"Maybe they just went in to ask her some questions." John said. "Listen, you need to get your mind off of this. Greg, got any interesting cases lying in wait for the one and only consulting detective?"

"Yeah, now that you mention it. Here's something definitely worth looking at." Lestrade shifted gears and pulled out his phone. "Just got this update today. Your brother told me to let you know." Lestrade gestured at Sherlock. Sherlock rolled his eyes.

"Apparently, they traced the video source." "The video of Moriarty?" Sherlock asked, suddenly interested.

"Yeah. It seems like it came from somewhere in the Marylebone district, which…"

"Baker street." said John. "Why would Moriarty make it seem like it came from 221B?"

"To make it seem like I created the video to protect myself from being sent away on that suicide mission." stated Sherlock plainly. "Really, that seems rather amateurish of him. There's something peculiar about this whole situation."

"Well?" Lestrade asked.

"Well, what? I don't have time for vague or unintelligible questions."

"You think he's actually alive?"

"Not sure." Sherlock bit his lip in frustration. "But whether alive or dead, he's planned something big. This isn't the end of it."

"But if it isn't Moriarty, then who could it be? Who would he leave this 'big plan' with?" said Lestrade, just as confused as ever. He never seemed to pick up on anything.

"I don't know, but that's why I'm here, isn't it?" Sherlock grinned for the first time since the incident at Bart's. Unfortunately, that would be the last time he would smile for the next few weeks to come.

At that moment, the doctor that had spoken to them before came out of the room, but this time the optimism had faded out of his eyes. Sherlock stood up and the three turned to him, concerned.

"I have some unexpected and difficult news for you gentlemen." The doctor said as he set down his clipboard and put his hands in his pockets. "I'm sorry to tell you this, but I don't think Ms. Hooper will wake up for a while."

"First of all, it's _Doctor_ Hooper." Sherlock said, his patience wearing thin. "Secondly, why? What happened?"

"We're not entirely sure, but she's gone into a low-level coma."

"What?" said both John and Greg simultaneously. Sherlock, however, just stared quite blankly.

"Don't worry, it's not too bad. I would say only a 10 on the Glasgow scale. She still has reflexes and responds to pain stimulus, but not to voice or soft touch."

John looked thoroughly confused (however, he rarely looks differently). "How did this happen? I thought you said it wasn't serious."

"There must be a stronger underlying cause that we haven't found yet." The doctor said apologetically. "My hunch is that there is a toxin present that caused the cardiac response and the hypoxemia, and that the extreme hypoxemia caused her to slip into a comatose state of consciousness. The most important thing is that she doesn't seem to have any brain damage, so we expect that this will be short lived as long as we can find the source and rid her body of the toxin."

"Well, I guess that's a good thing. Silver lining, eh?" said Greg hopefully. "How long do you think it will last?"

"Not sure, comatose patients are very hard to judge."

"Geez" John placed his hands on his hips and turned to Sherlock, who was still staring blankly forward. "How could something have gotten into her system so fast?"

"Don't act like you don't already know, John." Sherlock said, speaking for the first time.

"OK, so you're saying that Moriarty poisoned her, is that what you're saying, Sherlock?"

"Jesus Christ, are you serious?" Lestrade gasped.

"I don't know, Sherlock, it could be just a coincidence." John said, hoping that what he said was true, though he was pretty sure Sherlock was right. He almost always was, which didn't help with his ego or social skills.

"You know what we say about coincidences, John." Sherlock said intently, with that determined look in his eyes that John knew all too well. "The universe is rarely so lazy."

With that, Sherlock turned quickly on his heels and raced down the stairs.

As both John and Greg watched him go, Greg asked "Where do you think he's off to?"

"Christ knows." John said and ran after Sherlock, only to find him taking off in a cab, not wanting to be followed.

 ** _Day 1: 3:18pm: St. Bartholomew's Hospital_**

"Something, something, there must have been something I missed!" Sherlock hissed through clenched teeth as he stormed into the lab that he and Molly had been in only hours before.

He tore through all of the chemicals on the lab bench and hastily decided that nothing there could have caused it. Sherlock then quickly moved towards the office and searched through her desk. Nothing out of the ordinary: just basic office supplies, a couple pictures, and an uneaten lunch. Frustrated, Sherlock dug through the bin next to her desk. No food wrappers, only tissues and papers. As he stood up, he noticed a refillable water bottle and a mug, both only half full.

 _This is it_. It had to be. Quickly, Sherlock brought both the specimens over to the lab bench, took samples, and got to work. He ran chemical analyses through the computer and examined both the water and the tea under the microscope while he was waiting for the results. While waiting, his mind wandered to the topic of Moriarty.

If this was Moriarty (and he was sure it was), why would he target Molly? Sherlock never gave any indication whatsoever to just how important Molly was to him. And that was the point. Her safety was most important. John, Mary, Mycroft, and even Mrs. Hudson could handle themselves in a situation like this, but Molly couldn't. She's delicate, and frankly hopeless in precarious situations. Like he had said before, she was the one person that mattered the most, which Moriarty hadn't realized, and it had to stay that way until the final problem was solved. Maybe after that…

 _No, focus._ He told himself. _Focus on the problem at hand._

Just then, the computer beeped with the analyses results: Nothing. Absolutely nothing in the water from the bottle. The only thing slightly strange about the contents of the tea was the higher-than-usual concentration of grayanotoxins, but these chemicals were commonly found in honey from certain flowers. They could make people sick in a high enough amount, but Sherlock waved it away as irrelevant.

There was nothing. Nothing unusual about the water or tea. Frustrated, Sherlock slammed his fist on the table and went back to the microscope, desperately hoping there was something he missed.

As it turned out, the problem was staring right at him. Literally.

"Aw, poor little Sherly. His precious girlfriend is sick and he doesn't know what to do. Did you miss me Sherlock? I certainly missed you."

** _Thank you all for reading! Please, leave any comments you have below - every opinion is appreciated!**_


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